Opportunities for applying molecular genetics
If simple phenotype guided selection is used in isolation
there are inevitably some selection choices that will have conflicting outcomes, considering the diverse range of
traits that are important at different levels of the
production chain. For example, alleles of a particular gene
may be beneficial for one trait, but have negative effects on
another. In most cases, different genes will be involved in
controlling different traits. However, when the genes
controlling different traits are located very close together
on a chromosome it may appear that only one locus
controls both traits because alleles at linked loci will
generally be inherited together. Even with very closely
linked genes, the alleles that are found together in the
progeny of a particular individual will change because of
recombination between them (Fig. 1). Knowing the alleles
at particular genetic loci will enable the identification of
individuals that carry the beneficial alleles and allow for
direct selection of genetically superior animals at several
loci simultaneously. Therefore, in theory at least, a strategy
to select for improved performance in a number of traits
could be developed using genetic markers, even when at
the phenotypic level the traits may seem to be in conflict.
The major challenge that faces molecular geneticists is to
identify markers for genes that control the phenotypic
variation in the target traits. Two types of marker can be
considered. First, markers that are sufficiently close to the
trait gene on the chromosome such that, in most cases,
alleles at the marker and the trait gene are inherited
together. This type of marker is called a linked marker. At
the population level alleles at linked markers cannot be
used to predict the phenotype until the association
between alleles at the marker and alleles at the trait-gene is
known (called ‘phase’). To determine phase, inheritance of
the marker and trait gene has to be studied in a family.
However, information on phase is only valid within that
family and may change in subsequent generations through
recombination. The second type of marker is a functional polymorphism in the gene that controls variation in the
trait. These markers are called ‘direct’ markers. Once the
functional polymorphism is known it is possible to predict
the effect of particular alleles in all animals in a population,
without first having to determine the phase. Therefore,
‘direct’ markers are more useful than ‘linked’ markers for
predicting the phenotypic variation of target traits within a
population (7).